Question: R: oligo packages install error
0
gravatar for get3232
3 months ago by
get32320
get32320 wrote:

ERROR MESSAGES

=====================================================
> BiocManager::install("oligo")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'oligo'
also installing the dependencies ‘RCurl’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘oligoClasses’

URL 'https://cloud.r-project.org/src/contrib/RCurl_1.95-4.12.tar.gz'을 시도합니다
Content type 'application/x-gzip' length 916763 bytes (895 KB)
==================================================
downloaded 895 KB

URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/GenomeInfoDb_1.20.0.tar.gz'을 시도합니다
Content type 'application/x-gzip' length 3405894 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/GenomicRanges_1.36.0.tar.gz'을 시도합니다
Content type 'application/x-gzip' length 1160485 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/SummarizedExperiment_1.14.0.tar.gz'을 시도합니다
Content type 'application/x-gzip' length 1488171 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/oligoClasses_1.46.0.tar.gz'을 시도합니다
Content type 'application/x-gzip' length 372116 bytes (363 KB)
==================================================
downloaded 363 KB

URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/oligo_1.48.0.tar.gz'을 시도합니다
Content type 'application/x-gzip' length 28421048 bytes (27.1 MB)
==================================================
downloaded 27.1 MB

* installing *source* package ‘RCurl’ ...
** 패키지 ‘RCurl’는 성공적으로 압축해제되었고, MD5 sums 이 확인되었습니다
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/cy/R/x86_64-pc-linux-gnu-library/3.6/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/cy/R/x86_64-pc-linux-gnu-library/3.6/GenomeInfoDb’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/cy/R/x86_64-pc-linux-gnu-library/3.6/GenomicRanges’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/cy/R/x86_64-pc-linux-gnu-library/3.6/SummarizedExperiment’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’ are not available for package ‘oligoClasses’
* removing ‘/home/cy/R/x86_64-pc-linux-gnu-library/3.6/oligoClasses’
ERROR: dependency ‘oligoClasses’ is not available for package ‘oligo’
* removing ‘/home/cy/R/x86_64-pc-linux-gnu-library/3.6/oligo’

The downloaded source packages are in
    ‘/tmp/RtmpmnZOmY/downloaded_packages’
installation path not writeable, unable to update packages: C50, Cubist, data.table, e1071, Formula, glue, inum, libcoin,
  magrittr, mvtnorm, partykit, plyr, Rcpp, reshape2, RInside, RSNNS, stringi, stringr, xgboost, boot, class, codetools,
  foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nnet, spatial, survival
경고메시지(들): 
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘oligoClasses’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘oligo’ had non-zero exit status
===================================================================
version : 3.6.1

How can I fixed it? please, check this error quickly, Thank you so much

oligo error packages • 107 views
ADD COMMENTlink modified 3 months ago by Martin Morgan ♦♦ 23k • written 3 months ago by get32320
Answer: R: oligo packages install error
0
gravatar for Martin Morgan
3 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Start with the first error, and the first package that fails

** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’

Your system requires the system dependency libcurl, and it needs the development headers for that. The first two answer to this StackOverflow question might point you in the right direction; we would need to know the version of linux you're using to be more helpful.

ADD COMMENTlink written 3 months ago by Martin Morgan ♦♦ 23k
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